Classification of CRISPR/Cas system and its application in tomato breeding

CRISPR technologies and the search for the PAM-free nuclease

(2021) Daphne Collias et al.   Nature Communications

Genome editing of polyploid crops: prospects, achievements and bottlenecks

(2021) Jan G. Schaart et al.   TRANSGENIC RESEARCH

RNA-Targeting CRISPR–Cas Systems and Their Applications

(2020) Michal Burmistrz et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Allelic mutations in the Ripening-inhibitor (RIN) locus generate extensive variation in tomato ripening

(2020) Yasuhiro Ito et al.   PLANT PHYSIOLOGY

CRISPR/Cas9-Mediated SlMYC2 Mutagenesis Adverse to Tomato Plant Growth and MeJA-Induced Fruit Resistance to Botrytis cinerea

(2020) Pan Shu et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

An engineered ScCas9 with broad PAM range and high specificity and activity

(2020) Pranam Chatterjee et al.   NATURE BIOTECHNOLOGY

CRISPR/Cas9-targeted mutagenesis of the tomato susceptibility gene PMR4 for resistance against powdery mildew

(2020) Miguel I. Santillán Martínez et al.   BMC PLANT BIOLOGY

CRISPR/Cas9 targeted mutagenesis of SlLBD40, a lateral organ boundaries domain transcription factor, enhances drought tolerance in tomato

(2020) Lun Liu et al.   PLANT SCIENCE

Gene Editing in Plants– Progress and Challenges

(2019) Yanfei Mao et al.   National Science Review

Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems

(2019) Ashot Papikian et al.   Nature Communications

CRISPR/Cas9-Mediated SlNPR1 mutagenesis reduces tomato plant drought tolerance

(2019) Rui Li et al.   BMC PLANT BIOLOGY

European Court of Justice delivers no justice to Europe on genome‐edited crops

(2019) Alan H. Schulman et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-Editing Technologies: Concept, Pros, and Cons of Various Genome-Editing Techniques and Bioethical Concerns for Clinical Application

(2019) Sikandar Hayat Khan   Molecular Therapy-Nucleic Acids

Genome-editing technologies: the gap between application and policy

(2019) Gousi Li et al.   Science China-Life Sciences

RNA Interference (RNAi) Screening inDrosophila

(2018) Florian Heigwer et al.   GENETICS

Precise A·T to G·C Base Editing in the Rice Genome

(2018) Kai Hua et al.   Molecular Plant

Designer epigenome modifiers enable robust and sustained gene silencing in clinically relevant human cells

(2018) Tafadzwa Mlambo et al.   NUCLEIC ACIDS RESEARCH

OUP accepted manuscript

(2018)   PLANT AND CELL PHYSIOLOGY

A Novel Tomato Fusarium Wilt Tolerance Gene

(2018) Cahya Prihatna et al.   Frontiers in Microbiology

Lycopene Is Enriched in Tomato Fruit by CRISPR/Cas9-Mediated Multiplex Genome Editing

(2018) Xindi Li et al.   Frontiers in Plant Science

RNA Interference (RNAi) Screening inDrosophila

(2018) Florian Heigwer et al.   GENETICS

Knockout of SlMAPK3 Reduced Disease Resistance to Botrytis cinerea in Tomato Plants

(2018) Shujuan Zhang et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Reduction of Tomato-Plant Chilling Tolerance by CRISPR–Cas9-Mediated SlCBF1 Mutagenesis

(2018) Rui Li et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Design of a bacterial speck resistant tomato by CRISPR/Cas9-mediated editing of SlJAZ2

(2018) Andrés Ortigosa et al.   PLANT BIOTECHNOLOGY JOURNAL

PAM identification by CRISPR-Cas effector complexes: diversified mechanisms and structures

(2018) Daniel Gleditzsch et al.   RNA Biology

Tomato DCL2b is required for the biosynthesis of 22-nt small RNAs, the resulting secondary siRNAs, and the host defense against ToMV

(2018) Tian Wang et al.   Horticulture Research

Target-Specific Precision of CRISPR-Mediated Genome Editing

(2018) Anob M. Chakrabarti et al.   MOLECULAR CELL

Domestication of wild tomato is accelerated by genome editing

(2018) Tingdong Li et al.   NATURE BIOTECHNOLOGY

De novo domestication of wild tomato using genome editing

(2018) Agustin Zsögön et al.   NATURE BIOTECHNOLOGY

Enhanced genome editing in rice using single transcript unit CRISPR-Lb Cpf1 systems

(2018) Rongfang Xu et al.   PLANT BIOTECHNOLOGY JOURNAL

Functionally diverse type V CRISPR-Cas systems

(2018) Winston X. Yan et al.   SCIENCE

Rapid and user-friendly open-source CRISPR/Cas9 system for single- or multi-site editing of tomato genome

(2018) Nan Hu et al.   Horticulture Research

Reduced Drought Tolerance by CRISPR/Cas9-Mediated SlMAPK3 Mutagenesis in Tomato Plants

(2017) Liu Wang et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

A technological and regulatory outlook on CRISPR crop editing

(2017) Rea Globus et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

CRISPR-P 2.0: An Improved CRISPR-Cas9 Tool for Genome Editing in Plants

(2017) Hao Liu et al.   Molecular Plant

Multiplex Gene Editing in Rice Using the CRISPR-Cpf1 System

(2017) Mugui Wang et al.   Molecular Plant

Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion

(2017) Yuan Zong et al.   NATURE BIOTECHNOLOGY

Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion

(2017) Zenpei Shimatani et al.   NATURE BIOTECHNOLOGY

Multiplexed CRISPR/Cas9-mediated metabolic engineering of γ-aminobutyric acid levels in Solanum lycopersicum

(2017) Rui Li et al.   PLANT BIOTECHNOLOGY JOURNAL

A multi-purpose toolkit to enable advanced genome engineering in plants

(2017) Tomas Cermak et al.   PLANT CELL

The RNA Editing Factor SlORRM4 Is Required for Normal Fruit Ripening in Tomato

(2017) Yongfang Yang et al.   PLANT PHYSIOLOGY

Targeted recombination between homologous chromosomes for precise breeding in tomato

(2017) Shdema Filler Hayut et al.   Nature Communications

Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes

(2017) Zhen Liang et al.   Nature Communications

Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity

(2017) Alexis C. Komor et al.   Science Advances

SlMAPK3 enhances tolerance to tomato yellow leaf curl virus (TYLCV) by regulating salicylic acid and jasmonic acid signaling in tomato (Solanum lycopersicum)

(2017) Yunzhou Li et al.   PLoS One

Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion

(2017) Vladimir Nekrasov et al.   Scientific Reports

Rapid breeding of parthenocarpic tomato plants using CRISPR/Cas9

(2017) Risa Ueta et al.   Scientific Reports

CRISPR/Cas9-induced Targeted Mutagenesis and Gene Replacement to Generate Long-shelf Life Tomato Lines

(2017) Qing-hui Yu et al.   Scientific Reports

PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease

(2016) Hui Yang et al.   CELL

Naturally Occurring Off-Switches for CRISPR-Cas9

(2016) April Pawluk et al.   CELL

Control of inflorescence architecture in tomato by BTB/POZ transcriptional regulators

(2016) Cao Xu et al.   GENES & DEVELOPMENT

CRISPR/Cas9 Platforms for Genome Editing in Plants: Developments and Applications

(2016) Xingliang Ma et al.   Molecular Plant

The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA

(2016) Ines Fonfara et al.   NATURE

New CRISPR–Cas systems from uncultivated microbes

(2016) David Burstein et al.   NATURE

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

A proposed regulatory framework for genome-edited crops

(2016) Sanwen Huang et al.   NATURE GENETICS

Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato

(2016) Sebastian Soyk et al.   NATURE GENETICS

CRISPR–Cas adaptation: insights into the mechanism of action

(2016) Gil Amitai et al.   NATURE REVIEWS MICROBIOLOGY

Tomato facultative parthenocarpy results from SlAGAMOUS-LIKE 6 loss of function

(2016) Chen Klap et al.   PLANT BIOTECHNOLOGY JOURNAL

Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage

(2016) F. Jiang et al.   SCIENCE

Correction of the auditory phenotype in C57BL/6N mice via CRISPR/Cas9-mediated homology directed repair

(2016) Joffrey Mianné et al.   Genome Medicine

Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species

(2016) April Pawluk et al.   Nature Microbiology

CRISPR/Cas9-mediated efficient and heritable targeted mutagenesis in tomato plants in the first and later generations

(2016) Changtian Pan et al.   Scientific Reports

CRISPR/Cas9-mediated mutagenesis of the RIN locus that regulates tomato fruit ripening

(2015) Yasuhiro Ito et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The CRISPR-Cas immune system: Biology, mechanisms and applications

(2015) Devashish Rath et al.   BIOCHIMIE

Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis

(2015) Sidi Chen et al.   CELL

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR

(2015) Michael Boettcher et al.   MOLECULAR CELL

High-Efficiency Genome Editing in Arabidopsis Using YAO Promoter-Driven CRISPR/Cas9 System

(2015) Liuhua Yan et al.   Molecular Plant

A Robust CRISPR/Cas9 System for Convenient, High-Efficiency Multiplex Genome Editing in Monocot and Dicot Plants

(2015) Xingliang Ma et al.   Molecular Plant

Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins

(2015) Joseph Bondy-Denomy et al.   NATURE

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Functional annotation of native enhancers with a Cas9–histone demethylase fusion

(2015) Nicola A Kearns et al.   NATURE METHODS

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Mechanism of foreign DNA recognition by a CRISPR RNA-guided surveillance complex from Pseudomonas aeruginosa

(2015) MaryClare F. Rollins et al.   NUCLEIC ACIDS RESEARCH

Development of germ-line-specific CRISPR-Cas9 systems to improve the production of heritable gene modifications inArabidopsis

(2015) Yanfei Mao et al.   PLANT BIOTECHNOLOGY JOURNAL

Concise Review: Modeling Multiple Sclerosis With Stem Cell Biological Platforms: Toward Functional Validation of Cellular and Molecular Phenotypes in Inflammation-Induced Neurodegeneration

(2015) Joshua C. Orack et al.   Stem Cells Translational Medicine

How and why does tomato accumulate a large amount of GABA in the fruit?

(2015) Mariko Takayama et al.   Frontiers in Plant Science

Genome-editing technologies and their potential application in horticultural crop breeding

(2015) Jin-Song Xiong et al.   Horticulture Research

The Role of the Epigenome in Gene Expression Control and the Epimark Changes in Response to the Environment

(2014) Michael J. Van Oosten et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Consistent and Heritable Alterations of DNA Methylation Are Induced by Tissue Culture in Maize

(2014) Scott C. Stelpflug et al.   GENETICS

RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus

(2014) Raymond H.J. Staals et al.   MOLECULAR CELL

CRISPR-P: A Web Tool for Synthetic Single-Guide RNA Design of CRISPR-System in Plants

(2014) Yang Lei et al.   Molecular Plant

Unravelling the structural and mechanistic basis of CRISPR–Cas systems

(2014) John van der Oost et al.   NATURE REVIEWS MICROBIOLOGY

Detection and characterization of spacer integration intermediates in type I-E CRISPR–Cas system

(2014) Zihni Arslan et al.   NUCLEIC ACIDS RESEARCH

The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation

(2014) Hui Zhang et al.   PLANT BIOTECHNOLOGY JOURNAL

DOWNY MILDEW RESISTANT 6 and DMR6-LIKE OXYGENASE 1 are partially redundant but distinct suppressors of immunity in Arabidopsis

(2014) Tieme Zeilmaker et al.   PLANT JOURNAL

Hairy Root Transformation Using Agrobacterium rhizogenes as a Tool for Exploring Cell Type-Specific Gene Expression and Function Using Tomato as a Model

(2014) M. Ron et al.   PLANT PHYSIOLOGY

Efficient Gene Editing in Tomato in the First Generation Using the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated9 System

(2014) C. Brooks et al.   PLANT PHYSIOLOGY

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Plant genome engineering in full bloom

(2014) Jorge Lozano-Juste et al.   TRENDS IN PLANT SCIENCE

CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea

(2013) Rotem Sorek et al.   Annual Review of Biochemistry

CRISPR interference: a structural perspective

(2013) Judith Reeks et al.   BIOCHEMICAL JOURNAL

Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

(2013) Albert W Cheng et al.   CELL RESEARCH

Powdery Mildew Resistance in Tomato by Impairment of SlPMR4 and SlDMR1

(2013) Robin P. Huibers et al.   PLoS One

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Plants regenerated from tissue culture contain stable epigenome changes in rice

(2013) Hume Stroud et al.   eLife

Molecular Mechanisms of Epigenetic Variation in Plants

(2012) Ryo Fujimoto et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structure and Mechanism of the CMR Complex for CRISPR-Mediated Antiviral Immunity

(2012) Jing Zhang et al.   MOLECULAR CELL

CRISPR Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader DNA by Cascade and Cas3

(2012) Edze R. Westra et al.   MOLECULAR CELL

MYC2: The Master in Action

(2012) Kemal Kazan et al.   Molecular Plant

Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system

(2012) Joe Bondy-Denomy et al.   NATURE

Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

(2012) G. Gasiunas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Epigenetics and crop improvement

(2012) Nathan M. Springer   TRENDS IN GENETICS

Nature and Intensity of Selection Pressure on CRISPR-Associated Genes

(2011) N. Takeuchi et al.   JOURNAL OF BACTERIOLOGY

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence

(2011) E. Semenova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers

(2010) Soley Gudbergsdottir et al.   MOLECULAR MICROBIOLOGY

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

Brassinosteroid: a biotechnological target for enhancing crop yield and stress tolerance

(2009) Uday K. Divi et al.   New Biotechnology

Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

(2008) J. Carte et al.   GENES & DEVELOPMENT

A One Pot, One Step, Precision Cloning Method with High Throughput Capability

(2008) Carola Engler et al.   PLoS One

Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

(2008) S. J. J. Brouns et al.   SCIENCE